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Öğe Allele Mining for Molecular Breeding in Potato(CRC Press, 2024) Naeem, Muhammad; Yavuz, Caner; Çalışkan, Mehmet EminPotato has great genetic diversity that has been lost during the process of domestication. Due to this constraint, modern breeding programs rely on limited genetic resources for the improvement of potato. Allele mining helps in the identification of target alleles, and novel genes of known functions along with their sequence within the diverse germplasm collections controlling key traits. The wild potato relatives and landraces found at the diversity center serve as excellent germplasm for exploring the allelic variation and candidate genes to develop allele-specific markers to screen against particular traits. Moreover, the availability of genome sequence in potato, especially for wild relatives, such as S. commersonii, provide insights into genome evolution and mining of significant genes/alleles associated with various traits of economic value. The current chapter highlights important genomic regions (genes/alleles) originated from wild potato germplasm conferring tolerance/resistance against abiotic, biotic and tuber-related characteristics. The understanding of natural allelic variation will prove to be worthy in marker-assisted selection and identification of new haplotypes. © 2024 selection and editorial matter, Chittaranjan Kole, Tusar Kanti Behera, and Prashant Kaushik; individual chapters, the contributors.Öğe An overview of genome-wide association mapping studies in Poaceae species (model crops: wheat and rice)(Springer, 2022) Zia, Muhammad Abu Bakar; Yousaf, Muhammad Farhan; Asim, Arslan; Naeem, MuhammadThere is a significant interest while utilizing association mapping technique to determine the genes which are accountable for numerical dissimilarity of the more complex characteristics with agronomic and evolutionary significance. Recently improvements have been made in genomic technology, which motivates for the exploitation of natural diversity, and establishment of more vigorous and strong statistical analysis methods. It creates association mapping technique more demanding and reasonable to plant research programs. Genome-wide association mapping technique recognizes quantitative trait loci (QTLs) by studying the marker-trait associations which could be credited to the power of linkage disequilibrium between different molecular markers and functional polymorphisms through a pool of diversified germplasm. In this review, we will describe an overview of genetic mapping and the current status of association mapping studies in model cereal crops i.e., wheat and rice.Öğe Application of SolCAP Genotyping in Potato (Solanum tuberosum L.) Association Mapping(NLM (Medline), 2023) Yousaf, Muhammad Farhan; Zia, Muhammad Abu Bakar; Naeem, MuhammadPotato variety development entails a number of breeding steps, as well as testing and, finally, commercialization. Historically, phenotypic assesment were carried out to select and germplasm development. The US Department of Agriculture (USDA) funded the Solanaceae Coordinated Agricultural Project (SolCAP) to decode genomic resources into tools that breeders and geneticists can use. This project resulted in the creation of a genome-wide single-nucleotide polymorphism (SNP) array that can be used to evaluate elite potato-breeding germplasm. This array was used to genotype a diverse panel of Solanum species, as well as numerous biparental, diploid, and tetraploid populations. It has high marker density to generate genetic maps that can be used to identify numerous quantitative trait loci (QTLs) for agronomic, quality, biotic, and abiotic resistance traits. Up to now, numerous QTLs for important traits have been identified using new diploid and tetraploid genetic maps. SNP markers were used to assess germplasm relationships and fingerprint varieties and identify candidate genes. The Infinium 8303 SolCAP Potato array offers a common set of SNP markers that can be used for mapping, germplasm assessment, and fingerprinting with confidence. This array has also been helpful in furthering our understanding of the potato genome. Furthermore, some other Infinium potato arrays (i.e., 12 K, 20 K, and 25 K) have been genotyped, and breeders can map quantitative trait loci (QTLs) across multiple populations to improve our understanding of economically important traits and lead to marker-assisted selection (MAS) and breeding and, ultimately, improved varieties. © 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.Öğe Association mapping of quality traits in potato (Solanum tuberosum L.)(Niğde Ömer Halisdemir Üniversitesi / Fen Bilimleri Enstitüsü, 2021) Naeem, Muhammad; Çalışkan, Mehmet EminPatates (Solanum tuberosum L.) yetiştiriciliğinde, geliştirilmiş yumru kalitesi her zaman elde edilmek istenen özelliklerden biri olmuştur. Bu çalışmanın amacı, 192 adet tetraploid patates genotipinden oluşan panelde ilişkilendirme haritalaması yöntemiyle 25K SolCAP dizisini kullanarak on iki önemli yumru kalitesi özelliği ile ilişkili SNP'leri belirlemektir. Fenotipleme, HPLC gibi yeni nesil platformlar kullanılarak stabilite analizi ile kararlı genotipleri ortaya çıkarmak için gerçekleştirildi. Bayes kümeleme yaklaşımı, STRUCTURE algoritması aracılığıyla değerlendirilen dört alt popülasyonu tanımlar. LD ve ilişkilendirme haritalaması için 13606 polimorfik SNP markör kullanılmıştır. LD analizi, patatesin ıslah sürecini yansıtan 2.31 Mbs düzeyinde bir çözünme ortaya çıkarmıştır. İlişkilendirme Haritalaması, sırasıyla eklemeli ve genel modellerle 215 ve 430 önemli SNP ortaya çıkaran 2 poliploid gen aksiyonu ile doğrusal karışık model (Q + K) kullanılarak gerçekleştirildi. Tanımlanan SNP'ler, nişasta biyosentezinin, karotenoid biyosentezi (bch), stres tepkileri ve suberin biyosentezinde yer alan transkripsiyon faktörleri (MYB, bHLH, bZIP) ile ilgili çok çeşitli gen fonksiyonlarına sahiptir. Bu çalışmada elde edilen bulgular sonucunda patateste kalite özellikleriyle ilgili seleksiyon markörlerinin geliştirilmesiyle genomik destekli ıslaha kaynak sağlanacaktır.Öğe Association mapping reveals novel genomic regions controlling some root and stolon traits in tetraploid potato (Solanum tuberosum L.)(Springer Heidelberg, 2021) Yousaf, Muhammad Farhan; Demirel, Ufuk; Naeem, Muhammad; Caliskan, Mehmet EminTuber crops have measurable biological variation in root and stolon phenotyping and thus may be utilized to identify genomic regions associated with these variations. This is the first comprehensive association mapping study related to potato root and stolon traits. A diverse panel of 192 tetraploid potato (Solanum tuberosum L.) genotypes were grown in aeroponics to reveal a biologically significant variation and detection of genomic regions associated with the root and stolon traits. Phenotyping of root traits was performed by image analysis software WinRHIZO (a root scanning method), and stolon traits was measured manually, while SolCAP 25K potato array was used for genotyping. Significant variation was observed between the potato genotypes for root and stolon traits along with high heritabilities (0.80 in TNS to 0.95 in SL). For marker-trait associations, Q + K linear mixed model was implemented and 50 novel genomic regions were detected. Significantly associated SNPs with stolon traits were located on chr 4, chr 6, chr 7, chr 9, chr 11 and chr 12, while those linked to root traits on chr 1, chr 2, chr 3, chr 9, chr 11, and chr 12. Structure and PCA analysis grouped genotypes into four sub-populations disclosing population genetic diversity. LD decay was observed at 2.316 Mbps (r(2) = 0.29) in the population. The identified SNPs were associated with genes performing vital functions such as root signaling and signal transduction in stress environments (GT-2 factors, protein kinases SAPK2-like and protein phosphatases StPP1), transcriptional and post-transcriptional gene regulation (RNA-binding proteins), sucrose synthesis and transporter families (UGPase, Sus3, SuSy, and StSUT1) and PVY resistance (Ry sto). The findings of our study can be employed in future breeding programs for improvement in potato production.Öğe COMPARISON OF METHODS FOR DRY MATTER CONTENT DETERMINATION IN POTATO USING MULTI-ENVIRONMENTS FIELD DATA AND STABILITY STATISTICS(Soc Field Crop Sci, 2020) Naeem, Muhammad; Caliskan, Mehmet EminTuber dry matter content (TDM) is considered as the main determinant of processed potato tuber quality. In order to investigate rapid, practicable and reliable methods for the measurement of TDM, a study was planned to compare three standard methods (digital potato hydrometer, moisture-drying on quartz seasand and oven-dry) among 189 diverse potato genotypes, grown under three environmental conditions (Hatay standard water application, Konya standard water application and Konya drought conditions). ANOVA revealed highly significant differences (p<0.01) in all treatments among tests, checks and tests vs check genotypes. Environmental conditions significantly affect the TDM, while methods showed differential response within the tested environments. A strong correlation (r) and high goodness of fit (R-2) was observed between seasand and hydrometer methods as compared to oven-dry method. Wide applicability and reliability of seasand and hydrometer methods were also confirmed by stability statistics. This study recommends seasand as an accurate and hydrometers as rapid method in contrast to oven dry method for the measurement of TDM. Parametric stability methods such as bi and S-di(2) identified stable genotypes with optimum TDM, that can serve as a useful resource for breeding of processing cultivars.Öğe Genetic engineering techniques in potato(Elsevier, 2024) Zia, Muhammad Abu Bakar; Ijaz, Muhammad; Sami-ul-Allah; Aslam, Roohi; Naeem, Muhammad; Gul, Alvina; Butt, Razmia SabahatPotato is the world's number one nongrain commodity and the fourth most common commodity overall after maize, rice, and wheat. In terms of cell culture, potato exhibits a high level of docility. It also has an extended history of applications in biotechnology for the improvement of crops. The recent genomic revolution has significantly enhanced the overall understanding of the genetic makeup of all crops. Crop genome sequences have reformed our view and understanding of genome association and genome development. Recent updated knowledge in markers along with advanced phenotyping, genotyping-by-sequencing (GBS), and genome-wide association studies (GWAS) has led to the development of new ways of determining marker-trait associations that can withstand genome-based breeding programs. The accessibility of sequencing of genomic data has permitted editing of the genome (localized mutagenesis) for obtaining sequences of genes that are anticipated by breeders. In the realm of potato breeding, some genetic features such as genomics, genetic mapping, and marker application have also given breeders tasks to accomplish. Several strategies have been formulated to describe potato loci, contender genes and alleles, and their associated genotypes and phenotypes. This chapter highlights how genomics technologies can be modified to meet the needs of potato breeders to enhance potato improvement through the use of next-generation phenotyping, GWAS, and genome editing tools. © 2024 Elsevier Inc. All rights reserved.Öğe Genome editing for nutrient use efficiency in crops(Springer International Publishing, 2022) Yağiz, Ayten Kübra; Yavuz, Caner; Naeem, Muhammad; Dangol, Sarbesh Das; Aksoy, EmrePlant breeders have concentrated on increasing the yields, and in turn, the production in the last century to meet the increasing food demand, while ignoring the nutrition values of staple food crops. However, the malnutrition pandemic showed us that plant breeding should also focus on enhancing the nutritional quality of staple foods. Therefore, crop biofortification is one of the major goals of today's agriculture to eliminate malnutrition in the world. There are different strategies of crop biofortification, ranging from conventional to molecular breeding to transgenics. On the one hand, crop breeding seems to be a logical strategy to develop new nutritious varieties, but it takes much longer and requires manpower. On the other hand, transgenic technologies can shorten the time to develop new varieties and require less effort. Even though the obvious advantages of the transgenic technologies, transgenic crop varieties cannot be taken to the market because of strong public opposition. For this very reason, genome editing can facilitate transgene-free variety production. CRISPR/Cas-based genome editing has been used in many aspects of plant science to understand the function of the gene(s), to develop stress-tolerant varieties, and of course to develop biofortified crops. This chapter describes crop biofortification studies using conventional transgenic and genome editing technologies. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2022. All rights reseverd.Öğe Growth and developmental responses of crop plants under drought stress: a review(LITHUANIAN RESEARCH CENTRE AGRICULTURE & FORESTRY, 2017) Anjum, Shakeel Ahmad; Ashraf, Umair; Zohaib, Ali; Tanveer, Mohsin; Naeem, Muhammad; Ali, Iftikhar; Nazir, UsmanWater deficit conditions are a bearing on plant growth and development leading to diminished crop productivity. However, improving the crop productivity is need of the time to sustain the food security under ever increasing world population. Drought episodes are increasing with varying intensity and duration. Drought stress imposes alterations in crucial plant growth and developmental processes, including germination, plant height, stem diameter, number of leaves, leaf size and area, dry matter production and partitioning, flower and fruit production, and maturity. Nonetheless, plants show some morphological changes to cope with drought stress by lowering water loss, enhanced water uptake and maintenance of tissue water status. Some plants complete their life cycle early before the onset of drought to escape water deficit conditions. Identification of effects of drought stress on morphological attributes and morphological changes in response to drought can be promising for selection and breeding of drought resistant genotypes.Öğe Overview on domestication, breeding, genetic gain and improvement of tuber quality traits of potato using fast forwarding technique (GWAS): A review(Wiley, 2021) Naeem, Muhammad; Demirel, Ufuk; Yousaf, Muhammad Farhan; Caliskan, Sevgi; Caliskan, Mehmet EminTuber quality is the subject of great interest among the processing industry and consumers worldwide. Being a polygenic trait, its enhancement requires a systematic understanding of their genetic complexity. Molecular genetics offered valuable solutions to the challenging endeavours of slow genetic gains in conventional potato breeding. With the advent of linkage maps, molecular markers and availability of next-generation sequencing (NGS) platforms, the plant breeding programmes worldwide have achieved faster genetic gain due to marker-assisted selection (MAS). Linkage mapping detects QTLs in biparental population; alternatively, genomic and phenotypic differences can be identified by extensive genotyping and phenotyping of a germplasm panel depicting natural biological diversity to reveal QTLs, in other words, marker-trait associations. Due to advancements in the fields of genome sequencing and bioinformatics, researchers have preferred to use the genome-wide association mapping (GWAS) method for detecting QTLs due to its higher resolution. In potato, GWAS identified causative allele(s)/loci and provides reliable platform for the development of diagnostic SNP markers by employing Infinium SolCAP SNP array. Later, KASP validation markers can be developed to be used as selection markers in order to bred improved cultivars. The current review focuses on recently used approaches for genetic analyses (linkage mapping or association mapping) regarding potato tuber quality traits, provides comprehensive knowledge about breeding, genetic gain, basic genetic and statistical GWAS concepts and subsequently highlights the genetic discoveries using GWAS and KASP markers.Öğe Potato taxonomy and wild relatives(Elsevier, 2022) Naeem, Muhammad; Maqbool, Amir; Aksoy, EmrePotato (Solanum tuberosum L.) is an essential ingredient of the human diet in many countries. It is considered one of the top promising crops to reduce human hunger and poverty in the world. As a staple, it is the third most-produced food crop in the world. First domesticated in the mountains of South America, nowadays potato is cultivated worldwide in 159 countries. Cultivated potato (S. tuberosum L.) and its wild relatives belong to the Solanum sect. Petota (Solanaceae), which includes approximately 110 Solanum species. The large genetic diversity in the Solanaceae can be used in potato breeding for the development of new elite varieties that are more yielding, nutritious, and resilient to environmental stresses. Many studies have investigated the germplasm diversity of wild potato relatives in the center of origin. This chapter summarizes the studies done on potato germplasm diversity in terms of agro-morphological, molecular characterization, and preservation. © 2023 Elsevier Inc. All rights reserved.Öğe Recent advances in potato (solanum tuberosum L.) breeding(Springer International Publishing, 2021) Aksoy, Emre; Demirel, Ufuk; Bakhsh, Allah; Zia, Muhammad Abu Bakar; Naeem, Muhammad; Saeed, Faisal; Çalişkan, SevgiPotato (Solanum tuberosum L.) is an annual dicotyledonous tuber crop originating from the Americas and now distributed all over the world. A member of the Solanaceae family, potato is the fourth most produced food crop and the first non-cereal crop in the world. Potato is a staple food with its high potentiality in fighting malnutrition in the world since potato tubers are known sources of vitamins, proteins, carbohydrates and minerals. Moreover, it generates higher yield compared to the other crops; hence, it is one of the most notable crops to eliminate hunger and poverty. Therefore, sustainable potato production is important for food security and social welfare in future climate-change scenarios. However, it is very sensitive to environmental conditions and climate change due to its shallow root system. Therefore, future potato breeding programs should focus on enhancement of abiotic and biotic stress tolerance by utilizing the natural germplasm conserved in different gene banks. Moreover, potato breeding should benefit from the effectiveness and ease of molecular techniques such as marker-assisted selection, genome-wide association studies, functional genomics and transgenics. Development of new potato varieties can also be achieved via genetic engineering and genome editing. Disease-free potato seed production requires integration of tissue culture methods in plant breeding. As a staple food for millions, the potato has an extraordinarily rich past, and a bright future. The demand for potato will increase in future, which will be the driving force behind the potato research. © Springer Nature Switzerland AG 2021.Öğe SNP Markers Associated with Some Root, Stolon, and Tuber Traits in Tetraploid Potatoes (Solanum tuberosum L.) Grown Under Diverse Growing Systems(Springer, 2024) Yousaf, Muhammad Farhan; Demirel, Ufuk; Naeem, Muhammad; Naawe, Eric Kuopuobe; Caliskan, Mehmet EminNumerous loci, environmental factors, and their interactions have an impact on the phenotypic diversity of several significant traits in plants. One approach put forth in recent years for genetic research and finding quantitative trait loci (QTLs) responsible for the specific trait is association mapping. The purpose of the current study was to pinpoint the genetic underpins of significant underground traits in potato. A panel of 192 diverse tetraploid potato genotypes from different countries were grown under different growing conditions (i.e., aeroponics and pot) to study root, stolon and tuber traits. Significant differences (P <= 0.01) were found between the genotypes for all examined traits, and the heritability (H-2) of the traits ranged from 0.74 to 0.94. Genotyping was carried out using the SolCAP 25K array. 21,226 polymorphic SNPs were used for association mapping of underground traits. A GWASpoly R package was implemented for the marker-trait associations, and 78 genomic regions were found associated with the traits under investigation.. The history of potato breeding was reflected in LD patterns. The identified SNPs have their putative gene functions related to the root and stolon architecture and tuber growth (i.e., WRKY transcription factor, MAPK, the GTP cyclohydrolase 1 (i.e., GTPCHI), Glutathionyl-hydroquinone reductase, and pyrophosphate-fructose 6-phosphate 1-phosphotransferase subunit alpha (PFPase). The results of the present study provides a framework that could be helpful for future potato breeding programs to increase tuber production and reduce the challenges of feeding the world's population in the years to come.
